rs1543505

chr14-22893419-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001077351.2(RBM23):c.*8311C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,126 control chromosomes in the GnomAD database, including 42,398 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.74 (42394 hom., cov: 32)
  • Exomes 𝑓: 0.83 (4 hom.)
• Consequence: RBM23 NM_001077351.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

RBM23 (HGNC:20155): (RNA binding motif protein 23) This gene encodes a member of the U2AF-like family of RNA binding proteins. This protein interacts with some steroid nuclear receptors, localizes to the promoter of a steroid- responsive gene, and increases transcription of steroid-responsive transcriptional reporters in a hormone-dependent manner. It is also implicated in the steroid receptor-dependent regulation of alternative splicing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM23	NM_001077351.2	c.*8311C>T		3_prime_UTR_variant	14/14	ENST00000359890.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM23	ENST00000359890.8	c.*8311C>T		3_prime_UTR_variant	14/14	1	NM_001077351.2	P2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113029 AN: 151996 Hom.: 42365 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.734

GnomAD4 exome AF: 0.833 AC: 10 AN: 12 Hom.: 4 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.744 AC: 113105 AN: 152114 Hom.: 42394 Cov.: 32 AF XY: 0.748 AC XY: 55645 AN XY: 74350

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.737

Alfa AF: 0.723 Hom.: 76336

Bravo AF: 0.747

Asia WGS AF: 0.886 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.70
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1543505; hg19: chr14-23362628;